Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains

Abstract

AbstractBackgroundVagococcus fluvialisis a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has been greatly understudied, with no complete genome assembly available to date, which is essential for the characterisation of the mobilome.ResultsWe sequenced and assembled de novo the complete genome sequences of fiveV. fluvialisisolates recovered from marine sponges. Pangenome analysis of theV. fluvialisspecies (total of 17 genomes) showed a high intraspecific diversity, with 45.5% of orthologous genes found to be strain specific. Despite this diversity, analyses of gene functions clustered allV. fluvialisspecies together and separated them from other sequencedVagococcusspecies.V. fluvialisstrains from different habitats were highly similar in terms of functional diversity but the sponge-isolated strains were enriched in several functions related to the marine environment. Furthermore, sponge-isolated strains carried a significantly higher number of mobile genetic elements (MGEs) compared to previously sequencedV. fluvialisstrains from other environments. Sponge-isolated strains carried up to 4 circular plasmids each, including a 48-kb conjugative plasmid. Three of the five strains carried an additional circular extrachromosomal sequence, assumed to be an excised prophage as it contained mainly viral genes and lacked plasmid replication genes. Insertion sequences (ISs) were up to five times more abundant in the genomes of sponge-isolated strains compared to the others, including several IS families found exclusively in these genomes.ConclusionsOur findings highlight the dynamics and plasticity of theV. fluvialisgenome. The abundance of mobile genetic elements in the genomes of sponge-isolatedV. fluvialisstrains suggests that the mobilome might be key to understanding the genomic signatures of symbiosis in bacteria.